From: Irene Newhouse (einew_at_hotmail.com)
Date: Sun Jan 22 2012 - 16:17:15 CST

The problem was that the directory I was in had been restored from a backup device. Even though nominally the permissions looked OK, somehow they weren't. chown -R to myself, chgrp -R to myself followed by chmod -R 775 for the entire dir solved the problem.

Irene

From: einew_at_hotmail.com
To: akohlmey_at_gmail.com
CC: vmd-l_at_ks.uiuc.edu
Subject: RE: vmd-l: VMD and Centos 6
Date: Sun, 22 Jan 2012 10:39:16 -1000

If I touch test.txt in the same dir from which I had this problem, a file IS created. I have no problem vi'ing a file & saving the changes. Here's the contents of the vmd console:
[newhoir_at_hals chikros]$ vmd
/usr/bin/which: no rlwrap in (/usr/local/krb5/bin:/usr/local/krb5/bin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/sbin:/usr/sbin:/sbin:/usr/local/bin/vmd:/opt/schro2010b:/opt/schro2010b/utilities:/usr/local/lib/dowhm/bin:/usr/local/bin:/usr/amber11/dat/leap/cmd:/usr/amber11/AmberTools/amberlite/bin:/opt/UCSF/Chimera64-1.5.2/bin:/usr/local/bin/ied-2.02:/usr/local/lib/dowhm/bin:/usr/local/lib/dowhm/bin/linux:/usr/local/bla/blast-2.2.24/bin:/usr/local/genthr/bin:/usr/lib/modeller9.10:/usr/lib/modeller9.10/bin:/usr/amber11/bin:/home/newhoir/hole2/exe:/home/newhoir/bin:/usr/local/bin/vmd:/opt/schro2010b:/opt/schro2010b/utilities:/usr/local/lib/dowhm/bin:/usr/local/bin:/usr/amber11/dat/leap/cmd:/usr/amber11/AmberTools/amberlite/bin:/opt/UCSF/Chimera64-1.5.2/bin:/usr/local/bin/ied-2.02:/usr/local/lib/dowhm/bin:/usr/local/lib/dowhm/bin/linux:/usr/local/bla/blast-2.2.24/bin:/usr/local/genthr/bin:/usr/lib/modeller9.10:/usr/lib/modeller9.10/bin:/usr/amber11/bin:/home/newhoir/hole2/exe)
Info) VMD for LINUXAMD64, version 1.9 (March 14, 2011)
Info) http://www.ks.uiuc.edu/Research/vmd/
Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
Info) Please include this reference in published work using VMD:
Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
Info) -------------------------------------------------------------
Info) Multithreading available, 4 CPUs detected.
Info) Free system memory: 23171MB (96%)
Info) No CUDA accelerator devices available.
Warning) Detected X11 'Composite' extension: if incorrect display occurs
Warning) try disabling this optional X server feature.
Info) OpenGL renderer: Software Rasterizer
Info) Features: STENCIL MDE CVA MTX NPOT PP PS GLSL(OVF)
Info) Full GLSL rendering mode is available.
Info) Textures: 2-D (4096x4096), 3-D (256x256x256), Multitexture (8)
Info) Dynamically loaded 2 plugins in directory:
Info) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile
vmd > Info) Using plugin pdb for structure file /home/newhoir/chikros/all.pdb
Info) Using plugin pdb for coordinates from file /home/newhoir/chikros/all.pdb
Info) Determining bond structure from distance search ...
Info) Analyzing structure ...
Info) Atoms: 51033
Info) Bonds: 35798
Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0
Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
Info) Residues: 15621
Info) Waters: 15286
Info) Segments: 1
Info) Fragments: 15301 Protein: 1 Nucleic: 0
Info) Finished with coordinate file /home/newhoir/chikros/all.pdb.
Info) Rendering current scene to 'vmdscene.dat' ...
ERROR) Could not open file vmdscene.dat in current directory for writing!
Info) Rendering complete.

I'm launching from the directory containing the pdb file I intend to render [highlighted in red - hope it comes through]. The Molecule File Browser correctly picks up the directory, as all.pdb is listed in the file list box, along with all the other files I know to be in that directory. As is apparent, it loaded perfectly. So I did some experimentation. If I do an rmsd with the RMSDTT & try to write the file, it's written. When I did an ls -l, I think I found a clue:

[newhoir_at_hals chikros]$ ls -l *.dat
-rw-rw-r--. 1 newhoir newhoir 729 Jan 22 10:16 trajrmsd.dat
-rwxr-xr-x. 1 root root 4170142 Jan 19 19:10 vmdscene.dat

As newhoir, I can't process vmdscene.dat. I installed vmd as root & it looks as if that was my mistake!
Thanks!
Irene

> Date: Sun, 22 Jan 2012 11:19:06 -0500
> Subject: Re: vmd-l: VMD and Centos 6
> From: akohlmey_at_gmail.com
> To: einew_at_hotmail.com
> CC: vmd-l_at_ks.uiuc.edu
>
> On Sat, Jan 21, 2012 at 11:49 PM, Irene Newhouse <einew_at_hotmail.com> wrote:
> > I just, unfortunately, 'upgraded' my OS to Centos 6 from Centos
> > 5.-something. I tried to render a VMD image using tachyon & got an error
> > message indicating rendering was impossible because VMD did not have
> > permission to write vmdscene.dat to the current directory. Has anyone
> > encountered this already, and what did you do to fix it? This was not a
> > problem with the previous version of Centos!
>
> i cannot imagine that this has anything to do with your
> software upgrade directly. it can be a side effect or
> totally unrelated. possible reasons are the following:
>
> - there is a hardware error on your hard drive carrying your
> home directory and it has been mounted read-only.
>
> - your (numerical) userid is different and thus you don't
> really own your home directory and anything underneath
> it anymore
>
> - you launched VMD in a way that '/' has become its
> current working directory, to which you have no write access.
>
> can you generate other files? e.g. using "touch some_file.txt"
>
> cheers,
> axel.
> >
> > Thanks!
> > Irene Newhouse
>
>
>
> --
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com http://goo.gl/1wk0
>
> College of Science and Technology
> Temple University, Philadelphia PA, USA.